C. Harmon TCGA Survival
BM
7/19/2021
C. Harmon TCGA Survival TRDV1, 2, 3
This is an analysis of public TCGA expression (RNAseq) data in BRCA, COAD, LUAD, OV and UCEC using TRDV1, TRDV2 and TRDV3.
We use univariate and multivariate approaches, and stratify the patient cohorts based on median and {rpart} methods.
Data was downloaded and curated using the tcgabiolinks_RNA.R script available from [our Github repo] [https://github.com/brucemoran/charmon_tcga]
Data are in ./TCGA_* directories in the same dir. Output is saved to those dirs in the ./TCGA_*/survival directories.
## [1] "Working on: TCGA_BRCA"
## [1] "Running rpart on: DSS"
## [1] "Working on: ENSG00000211804"
## [1] "Working on: ENSG00000211821"
## [1] "Working on: ENSG00000256590"
## [1] "Running rpart on: PFI"
## [1] "Working on: ENSG00000211804"
## [1] "Working on: ENSG00000211821"
## [1] "Working on: ENSG00000256590"
## [1] "Running rpart survival on: PFI"
## [1] "Data available for: ENSG00000211804"
## [1] "Data not available for: ENSG00000211821"
## [1] "Data not available for: ENSG00000256590"## [1] "Running median survival on: DSS"
## [1] "Data available for: ENSG00000211804"
## [1] "Data available for: ENSG00000211821"
## [1] "Data available for: ENSG00000256590"## [1] "Running median survival on: PFI"
## [1] "Data available for: ENSG00000211804"
## [1] "Data available for: ENSG00000211821"
## [1] "Data available for: ENSG00000256590"## [1] "Saving and returning data..."
## [1] "Working on: TCGA_COAD"
## [1] "Running rpart on: DSS"
## [1] "Working on: ENSG00000211804"
## [1] "Working on: ENSG00000211821"
## [1] "Working on: ENSG00000256590"
## [1] "Running rpart survival on: DSS"
## [1] "Data available for: ENSG00000211804"
## [1] "Data not available for: ENSG00000211821"
## [1] "Data not available for: ENSG00000256590"
## [1] "Running rpart on: PFI"
## [1] "Working on: ENSG00000211804"
## [1] "Working on: ENSG00000211821"
## [1] "Working on: ENSG00000256590"
## [1] "Running rpart survival on: PFI"
## [1] "Data available for: ENSG00000211804"
## [1] "Data not available for: ENSG00000211821"
## [1] "Data not available for: ENSG00000256590"
## [1] "Running median survival on: DSS"
## [1] "Data available for: ENSG00000211804"
## [1] "Data available for: ENSG00000211821"
## [1] "Data available for: ENSG00000256590"## [1] "Running median survival on: PFI"
## [1] "Data available for: ENSG00000211804"
## [1] "Data available for: ENSG00000211821"
## [1] "Data available for: ENSG00000256590"## [1] "Saving and returning data..."
## [1] "Working on: TCGA_LUAD"
## [1] "Running rpart on: DSS"
## [1] "Working on: ENSG00000211804"
## [1] "Working on: ENSG00000211821"
## [1] "Working on: ENSG00000256590"
## [1] "Running rpart survival on: DSS"
## [1] "Data available for: ENSG00000211804"
## [1] "Data not available for: ENSG00000211821"
## [1] "Data available for: ENSG00000256590"
## [1] "Running rpart on: PFI"
## [1] "Working on: ENSG00000211804"
## [1] "Working on: ENSG00000211821"
## [1] "Working on: ENSG00000256590"
## [1] "Running rpart survival on: PFI"
## [1] "Data available for: ENSG00000211804"
## [1] "Data not available for: ENSG00000211821"
## [1] "Data not available for: ENSG00000256590"
## [1] "Running median survival on: DSS"
## [1] "Data available for: ENSG00000211804"
## [1] "Data available for: ENSG00000211821"
## [1] "Data available for: ENSG00000256590"## [1] "Running median survival on: PFI"
## [1] "Data available for: ENSG00000211804"
## [1] "Data available for: ENSG00000211821"
## [1] "Data available for: ENSG00000256590"## [1] "Saving and returning data..."
## [1] "Working on: TCGA_OV"
## [1] "Running rpart on: DSS"
## [1] "Working on: ENSG00000211804"
## [1] "Working on: ENSG00000211821"
## [1] "Working on: ENSG00000256590"
## [1] "Running rpart survival on: DSS"
## [1] "Data available for: ENSG00000211804"
## [1] "Data not available for: ENSG00000211821"
## [1] "Data available for: ENSG00000256590"
## [1] "Running rpart on: PFI"
## [1] "Working on: ENSG00000211804"
## [1] "Working on: ENSG00000211821"
## [1] "Working on: ENSG00000256590"
## [1] "Running rpart survival on: PFI"
## [1] "Data available for: ENSG00000211804"
## [1] "Data available for: ENSG00000211821"
## [1] "Data available for: ENSG00000256590"
## [1] "Running median survival on: DSS"
## [1] "Data available for: ENSG00000211804"
## [1] "Data available for: ENSG00000211821"
## [1] "Data available for: ENSG00000256590"## [1] "Running median survival on: PFI"
## [1] "Data available for: ENSG00000211804"
## [1] "Data available for: ENSG00000211821"
## [1] "Data available for: ENSG00000256590"## [1] "Saving and returning data..."
## [1] "Working on: TCGA_UCEC"
## [1] "Running rpart on: DSS"
## [1] "Working on: ENSG00000211804"
## [1] "Working on: ENSG00000211821"
## [1] "Working on: ENSG00000256590"
## [1] "Running rpart survival on: DSS"
## [1] "Data available for: ENSG00000211804"
## [1] "Data not available for: ENSG00000211821"
## [1] "Data not available for: ENSG00000256590"
## [1] "Running rpart on: PFI"
## [1] "Working on: ENSG00000211804"
## [1] "Working on: ENSG00000211821"
## [1] "Working on: ENSG00000256590"
## [1] "Running rpart survival on: PFI"
## [1] "Data available for: ENSG00000211804"
## [1] "Data available for: ENSG00000211821"
## [1] "Data not available for: ENSG00000256590"
## [1] "Running median survival on: DSS"
## [1] "Data available for: ENSG00000211804"
## [1] "Data available for: ENSG00000211821"
## [1] "Data available for: ENSG00000256590"## [1] "Running median survival on: PFI"
## [1] "Data available for: ENSG00000211804"
## [1] "Data available for: ENSG00000211821"
## [1] "Data available for: ENSG00000256590"
## [1] "Saving and returning data..."